#tissueclearing — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #tissueclearing, aggregated by home.social.
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This week I had the pleasure of attending the #MesoSPIM Symposium in Zürich, Switzerland - and what an experience it's been! Top-notch presentations, great posters and great chats with my fellow #lightsheet #microscopy and #tissueclearing nerds. You know it's a good conference when you come back with a full notebook and a head fizzing with ideas on what to do next.
I could make the night train journey there thanks to @Co_Biologists's DMM Conference Travel Grant - much appreciated! -
New publication from Kwanghun Chung lab at MIT improves on their SWITCH approach and eFLASH stochastic electrotransport to improve antibody labeling by gradually shifting the microenvironment. Looks interesting, I wonder how well it can be adapted to other labeling protocols.
Uniform volumetric single-cell processing for organ-scale molecular phenotyping
Yun et al., Nature Biotechnology 2025
https://doi.org/10.1038/s41587-024-02533-4#neuroscience #tissueclearing #lightsheet #microscopy #fluorescenceFriday
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Wow, TRISCO (née TRIC-DISCO) is out in Science! This cool approach allows imaging of mRNA transcripts throughout the cleared mouse brain. It uses a signal amplification step with in situ Hybridization Chain Reaction (isHCR) and combines it with DISCO-style solvent-based #tissueclearing to make the brain transparent.
Whole-brain spatial transcriptional analysis at cellular resolution
Kanatani et al., Science 2024
https://doi.org/10.1126/science.adn9947 -
In case anyone was following the recent Science paper about using Tartrazine for #tissueclearing, apparently there is at least one (competing) group that couldn't reproduce it and wrote a preprint about it:
Tartrazine cannot make live tissues transparent
https://doi.org/10.1101/2024.09.29.615648Discussion on Pubpeer, including the Tartrazine paper's author's response:
https://pubpeer.com/publications/81314BB3706B3D6ADAD49F301B2FA5 -
New solvent-based #tissueclearing protocol claims reduced tissue distortion: Dehydration/delipidation with Hexanediol, tert-Butanol and N-butyldiethanolamine, and clearing with Benzyl Benzoate / PEGMA / N-butyldiethanolamine.
SOLID: minimizing tissue distortion for brain-wide profiling of diverse architectures
Zhu et al., Nature Comms 2024
https://doi.org/10.1038/s41467-024-52560-7 -
New #tissueclearing #preprint uses a custom mouse behaviour + deep-learning c-Fos analysis pipeline to compare several different Serotonin receptor agonists / antagonists in mice.
Concerted modulation of spontaneous behavior and time-integrated whole-brain neuronal activity by serotonin receptors
Friedmann et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.08.02.606282#lightsheet #microscopy #serotonin #neuroscience #preprint #brainmapping
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New #tissueclearing paper checks oligodendrocyte distribution throughout the entire mouse brain. Looks pretty neat!
Brain-wide mapping of oligodendrocyte organization and oligodendrogenesis across the murine lifespan
Xu et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.09.06.611254Github: https://github.com/yxu233/Xu_Bergles_brainwide_oligo_map
#neuroscience #lightsheet #microscopy #preprint #oligodendrocyte #myelination
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This preprint looks like a conceptual advance for deeper staining (also in human tissue) and multi-round multiplexed immunostaining with BABB clearing.
INSIHGT: Accessible multimodal systems biology with quantitative molecular phenotyping in 3D
Yau et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.05.24.595771#tissueclearing #lightsheet #microscopy #neuroscience #FluorescenceFriday
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Landmarking via UV-activatable dye makes mapping between light-sheet and confocal imaging possible
Correlative multiscale 3D imaging of mouse primary and metastatic tumors by sequential light sheet and confocal fluorescence microscopy
Zheng et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.05.14.594162 -
Interesting new #preprint about #tissueclearing and #lightsheet #microscopy in mouse ovaries. Complete with #napari-based deep-learning pipeline and detailed build instructions for 3D-printed sample chambers for solvent-cleared samples, so they can be viewed under a #confocal!
OoCount: A machine-learning based approach to mouse ovarian follicle counting and classification
Folts et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.05.13.593993v1 -
Very excited that our whole-mouse-brain analysis pipeline - DELiVR - is published now at Nature Methods. With DELiVR, we built an open-source, easy-to-use pipeline for analyzing image stacks from cleared mouse brains.
Paper: https://www.nature.com/articles/s41592-024-02245-2
Code: https://github.com/erturklab/delivr_cfos
Docker containers, test dataset, handbook: https://www.discotechnologies.org/DELiVR/ -
Interesting #preprint: New mouse brain atlas links high-resolution MRI and light-sheet imaging, finally placing Allen Brain Atlas coordinates in stereotaxic space.
#tissueclearing was done via LifeCanvas and includes 17 common neuron type markers:
Preprint: https://www.biorxiv.org/content/10.1101/2024.03.28.587246v1.full
Atlas + webviewer here (requires registration): https://civmimagespace.civm.duhs.duke.edu
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Very cool new #tissueclearing #preprint - a clearing protocol for marine invertebrates aptly named See-Star.
Works on echinoderms and molluscs (i.e. sea stars, sea urchins, slugs and cuttlefish). I wonder whether it also works on terrestrial snails then?
See-Star: a versatile hydrogel-based protocol for clearing large, opaque and calcified marine invertebrates
Clarke et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.03.16.585344v1 -
Very nice work on #tissueclearing and #lightsheet #microscopy:
This technique (TESOS) brings resin embedding to solvent-cleared samples. The resulting #organogels are stable enough to allow block-face imaging with an oblique LSM. Already pretty big with whole adult mice, but I'd love to see this scaled up to human-organ size.
Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system
Yi et al., Cell Research 2024
https://doi.org/10.1038/s41422-023-00867-3 -
Really cool #lightsheet #microscopy application:
An atlas of the developing mouse brain (DevATLAS from Yongsoo Kim's lab), combined with a new neuronal activity reporter line (Npas4-Cre), shows the order in which brain regions become active in the first postnatal weeks.
(And they have #ephys and #rnaseq too!)
Spatiotemporal Mapping and Molecular Basis of Whole-brain Circuit Maturation
Xue et al., preprint on biorxiv, 2024
https://doi.org/10.1101/2024.01.03.572456 -
Interesting #multiplexing datapoint: This preprint describes a straightforward multiplex #microscopy strategy - Image 3 channels, blast sample with bright light until it's bleached, then re-stain. Works with 400 µm sections in fructose-based #tissueclearing solution.
Increased multiplexity in optical tissue clearing-based 3D immunofluorescence microscopy of the tumor microenvironment by LED photobleaching
Zheng et al., preprint at biorxiv 2023
https://www.biorxiv.org/content/10.1101/2023.11.29.569277v2?ct= -
Check out our lab's #newpaper in @cellpress Cell:
We found that the skull is special - its marrow is a special immunologic niche. Skull #Immune #cells can move to the meninges via skull-meninges connections, which we found both in mice and humans with #tissueclearing and #lightsheet #microscopy.
We also bring #proteomics and #PETimaging to the mix!Paper: https://doi.org/10.1016/j.cell.2023.07.009
Explainer thread:
https://bird.makeup/users/erturklab/statuses/1689293936185991169